THE CORPORATE LIBRARY

Related Party Transactions and Outside Related Director Information

Affymetrix, Inc. (AFFX)

5/1/2006 Proxy Information

Mr. Singer was President and Chief Executive Officer of Affymetrix from 1993 to June 1995 and served as Vice Chairman of Affymetrix, Inc. from July 1995 to April 1996.

John D. Diekman served as Chief Executive Officer of Affymetrix, Inc. from July 1995 to March 1997, Chairman from 1993 to August 1999 and Vice Chairman from July 1999 to December 1999.

In accordance with NASD listing standards, the Board conducts an appropriate review of all related party transactions required to be disclosed in this proxy statement for potential conflicts of interest situations on an ongoing basis and, all such transactions are approved by the Nominating and Corporate Governance Committee.

Extension of Credit

In July 2001, we made an extension of credit to Ms. Caulfield, our Executive Vice President and General Counsel, of up to $1.2 million in connection with her joining the Company. After this extension of credit was made, federal legislation was enacted prohibiting such extension of credit to executive officers and, accordingly, no future extensions of credit will be made by the Company to our executive officers, although the Company continues to honor its contractual obligations under the pre-existing extension of credit. In January 2004, Ms. Caulfield drew down the amount of $1.2 million under this extension of credit. Repayment is due on the earlier of January 2008 or the date Ms. Caulfield leaves the Company. Interest accrues at the IRS imputed rate of 3.5% and is payable by Ms. Caulfield starting this year.

Director and Executive Officer Indemnification Agreements

We have entered into indemnification agreements with each of our directors and executive officers. These agreements require us to indemnify our directors and executive officers to the fullest extent permitted by Delaware law.

Change in Control and Severance Plan

The Company has a change in control and severance plan that provides for the treatment of outstanding options and the receipt of severance benefits for employees and directors in the event of a transaction resulting in a change of control.

Under the plan, we are required to take any one or more of the following actions with respect to outstanding options in connection with a change of control:

á provide that the options shall be assumed, or equivalent options substituted, by the acquiring or succeeding corporation;

á following notice to the holders, provide that all of the unexercised options will become fully exercisable prior to the change of control and will terminate prior to the change of control to the extent unexercised; and/or

á if, under the terms of the transaction, our stockholders are to receive cash for their shares, provide that all option holders be cashed out by receiving a cash payment equal to the difference between the amount received by stockholders and the exercise price of such option.

Under certain circumstances, an employee who is terminated in connection with, or within 12 months following, a change of control will receive the full value of any unvested options as though vested as well as severance payments ranging from 3 monthsÕ salary to 18 monthsÕ salary (depending on the employee level), together with continued health benefits for the same period of time. To the extent that the law of the jurisdiction in which the employee is employed requires certain treatment with respect to options of employees who are terminated in connection with or within 12 months following a change of control, the employee will be entitled to the more beneficial treatment provided by the plan or applicable law.

The plan may be amended by the Board at any time prior to a change of control.

Perlegen Sciences, Inc.

Perlegen Sciences, Inc. is engaged in the business of scanning human genomes in an effort to identify variations and patterns within the human genome to discover genetic characteristics associated with disease, identify responsiveness to drug therapy and to create targeted medicines. We formed Perlegen in 2000 as a wholly-owned subsidiary and spun it off in March 2001 in a private equity financing which raised approximately $101 million. Following several subsequent rounds of private equity financings by Perlegen and our sale of a portion of our Perlegen shares to third parties for cash, our ownership interest, including that of our affiliates, was approximately 25% as of December 31, 2005. On April 7, 2006, Perlegen announced that it filed a registration statement with the Securities and Exchange Commission in connection with its proposed initial public offering. We also have certain commercial and licensing arrangements with Perlegen which are described in our Annual Report on Form 10-K for the fiscal year ended December 31, 2005.

Dr. Fodor, our chairman and CEO, also serves as chairman of Perlegen, and he holds shares representing approximately 0.84% of PerlegenÕs stock. We have the right to name two representatives to the Perlegen board of directors, and these positions are currently occupied by Dr. Fodor and Mr. Young, both members of our board of directors. Dr. Berg, who is another of our directors, is a member of PerlegenÕs scientific advisory board. Dr. Maxine F. Singer, who is the mother of Affymetrix director David B. Singer, is a member of PerlegenÕs board of directors. Mr. Young, Dr. Berg and Dr. Maxine F. Singer receive customary fees and hold options to purchase Perlegen stock as a result of their positions with Perlegen. Dr. Diekman and Dr. Berg, both members of our board of directors, each serve as trustees of separate trusts that invested an aggregate of approximately $577,000 in the private rounds of Perlegen financings in 2001, 2003 and 2005. Transactions between Perlegen and Affymetrix are overseen by a committee of the Affymetrix board of directors, whose members are Mr. Loucks, Dr. Desmond-Hellmann and Dr. Trice. None of these individuals hold positions with or securities of Perlegen.

4/27/2005 Proxy Information

During fiscal 2001 and 2002, the Company entered into agreements with certain of our executive officers to extend credit in connection with their joining the Company. After these extensions of credit were made, federal legislation was enacted prohibiting such extensions of credit to executive officers and accordingly, no future extensions of credit will be made by the Company to our executive officers, although the Company continues to honor its contractual obligations under pre-existing extensions of credit.

In July 2001, we made an extension of credit to Ms. Caulfield, our Executive Vice President and General Counsel, of up to $1.2 million in connection with her joining the Company. In January 2004, Ms. Caulfield drew down the amount of $1.2 million under this extension of credit. Repayment is due on the earlier of January 2008 or the date Ms. Caulfield leaves the Company. Interest accrues at the IRS imputed rate of 3.5% and is payable by Ms. Caulfield starting in 2006.

Under an extension of credit made by us on June 21, 2002, we made a $1,000,000 secured loan to assist Dr. Nicholls, previously our Chief Commercial Officer for Global Operations and Executive Vice President of Product Marketing & Development, in relocating his principal place of residence to the United States. On December 23, 2004, Dr. Nicholls repaid his entire outstanding balance on the loan. Pursuant to the terms of his loan, interest was forgiven by us for the years 2003 and 2004 in the aggregate amount of $67,600.

Perlegen Sciences, Inc. is engaged in the business of scanning human genomes in an effort to identify variations and patterns within the human genome to discover genetic characteristics associated with disease, identify responsiveness to drug therapy and to create targeted medicines. We formed Perlegen in 2000 as a wholly-owned subsidiary and in March 2001, we spun-out Perlegen as an independent entity. Concurrent with the 2001 spin-out, Perlegen raised approximately $101 million in a private financing and then raised an additional $32 million in a financing that was completed in 2003, reducing our ownership interest to below 45%. Our interest was reduced further as a result of our sale of a portion of our Perlegen shares for cash in December 2003 and January 2004. In February 2005, we purchased $2.0 million of Series D preferred stock in Perlegen's most recent private equity financing which Perlegen announced raised an aggregate of $74.0 million. As a result of this private equity placement, our ownership interest, including that of our affiliates, was reduced from approximately 40% as of December 31, 2004, to approximately 30% as of February 2005. We also have certain commercial and licensing arrangements with Perlegen which are described in our Annual Report on Form 10-K for the fiscal year ended December 31, 2004.

Dr. Fodor, our chairman and CEO, also serves as chairman of Perlegen, and he holds shares representing approximately 1.01% of Perlegen's stock. We have the right to name two representatives to the Perlegen board of directors, and these positions are currently occupied by Dr. Fodor and Mr. Young, both members of our board of directors. Dr. Berg, who is another of our directors, is a member of Perlegen's scientific advisory board. Dr. Maxine F. Singer, who is the mother of Affymetrix director David B. Singer, is a member of Perlegen's board of directors. Mr. Young, Dr. Berg and Dr. Maxine F. Singer receive customary fees and hold options to purchase Perlegen stock as a result of their positions with Perlegen. Dr. Diekman and Dr. Berg, both members of our board of directors, each serve as trustees of separate trusts that invested an aggregate of approximately $577,000 in the private rounds of Perlegen financings in 2001, 2003 and 2005. Transactions between Perlegen and Affymetrix are overseen by a committee of the Affymetrix board of directors, whose sole member is currently Mr. Loucks, who holds no position with or securities of Perlegen.

Mr. Diekman served as Chief Executive Officer of Affymetrix, Inc. from July 1995 to March 1997, Chairman from 1993 to August 1999 and Vice Chairman from July 1999 to December 1999.

4/29/2004 Proxy Information

Dr. Maxine F. Singer, who is the mother of Affymetrix director David B. Singer, is a member of Perlegen's board of directors. We own approximately 38% of the stock of Perlegen Sciences, Inc.

In accordance with NASD listing standards, effective January 2004, the Board will conduct an appropriate review of all related party transactions required to be disclosed in this proxy statement for potential conflicts of interest situations on an ongoing basis and, effective January 2004, all such transactions will be approved by the Audit Committee.

Extensions of Credit

During fiscal 2001 and 2002, the Company entered into agreements with certain of our executive officers to extend credit in connection with their joining the Company. After these extensions of credit were made, federal legislation was enacted prohibiting such extensions of credit to executive officers and accordingly, no future extensions of credit will be made by the Company, although the Company continues to honor its contractual obligations under pre-existing extensions of credit.

In July 2001, we made an extension of credit to Ms. Caulfield, our Executive Vice President and General Counsel, of up to $1.2 million in connection with her joining the Company. In January 2004, Ms. Caulfield drew down the amount of $1.2 million under this extension of credit. Repayment is due on the earlier of January 2008 or the date Ms. Caulfield leaves the Company. Interest accrues at the IRS imputed rate of interest in effect on the first day of the loan and is payable by Ms. Caulfield starting in 2006.

Under an extension of credit made by us on June 21, 2002, to Dr. Nicholls, our Chief Commercial Officer for Global Operations, we made a $1,000,000 secured loan to assist him in relocating his principal place of residence to the United States. The loan is due and payable on the earlier of January 7, 2008, the sale of the house or when Dr. Nicholls leaves the Company. Interest on the loan accrues at the rate equal to the IRS imputed rate per annum. In accordance with the terms of his extension of credit, up to 100% of the annual interest may be forgiven each year based on achievement of annual performance. In 2003, this resulted in interest of $33,800 being forgiven on this loan.

Director and Executive Officer Indemnification Agreements

We have entered into indemnification agreements with each of our directors and executive officers. These agreements require us to indemnify our directors and executive officers to the fullest extent permitted by Delaware law.

Change in Control and Severance Plan

The Company has a change in control and severance plan that provides for the treatment of outstanding options and the receipt of severance benefits for employees and directors in the event of a transaction resulting in a change of control.

Under the plan, we are required to take any one or more of the following actions with respect to outstanding options in connection with a change of control:

¥ provide that the options shall be assumed, or equivalent options substituted, by the acquiring or succeeding corporation;

¥ following notice to the holders, provide that all of the unexercised options will become fully exercisable prior to the change of control and will terminate prior to the change of control to the extent unexercised; and/or

¥ if, under the terms of the transaction, our stockholders are to receive cash for their shares, provide that all option holders be cashed out by receiving a cash payment equal to the difference between the amount received by stockholders and the exercise price of such option.

Under certain circumstances, an employee who is terminated in connection with, or within 12 months following, a change of control will receive the full value of any unvested options as though vested as well as severance payments ranging from 3 months' salary to 18 months' salary (depending on the employee level), together with continued health benefits for the same period of time. To the extent that the law of the jurisdiction in which the employee is employed requires certain treatment with respect to options of employees who are terminated in connection with or within 12 months following a change of control, the employee will be entitled to the more beneficial treatment provided by the plan or applicable law.

The plan may be amended by the Board at any time prior to a change of control.

Perlegen Sciences, Inc.

We own approximately 38% of the stock of Perlegen Sciences, Inc., which is engaged in the business of scanning human genomes in an effort to identify variations and patterns within the human genome to discover genetic characteristics associated with disease and responsiveness to drug therapy. We formed Perlegen in 2000 as a wholly-owned subsidiary. As a result of private financings completed by Perlegen in 2001 and 2003 raising an aggregate of about $130 million, our interest was diluted to 53% and then to below 45%. Our interest was reduced to its current level as a result of our sale of shares for cash in December 2003. We also have certain commercial and licensing arrangements with Perlegen which are described in our Annual Report on Form 10-K for the fiscal year ended December 31, 2003.

Dr. Fodor, our chairman and CEO, also serves as chairman of Perlegen, and he holds shares representing approximately 1.56% of Perlegen's stock. We have the right to name two representatives to the Perlegen board of directors, and these positions are currently occupied by Dr. Fodor and Mr. Young, both members of our board of directors. Dr. Berg, who is another of our directors, is a member of Perlegen's scientific advisory board. Dr. Maxine F. Singer, who is the mother of Affymetrix director David B. Singer, is a member of Perlegen's board of directors. Mr. Young, Dr. Berg and Dr. Maxine F. Singer receive customary fees and hold options to purchase Perlegen stock as a result of their positions with Perlegen. Dr. Diekman and Dr. Berg, both members of our board of directors, each serve as trustees of separate trusts that invested an aggregate of approximately $552,000 in the private rounds of Perlegen financings in 2001 and 2003. Transactions between Perlegen and Affymetrix are overseen by a committee of the Affymetrix board of directors whose sole member is currently Mr. Loucks, who holds no position with or securities of Perlegen.

4/29/2003 Proxy Information

On March 24, 2003, Dr. Fodor paid off a $500,000 housing loan, together with accrued interest, made by the Company to Dr. Fodor in April 1997. The loan bore interest at a rate of 6.49% and was due on the first to occur of April 11, 2003, the sale of the house, or termination of Dr. Fodor's employment.

Extension of Credit to Ms. Caulfield

In July 2001, the Company made an extension of credit to Ms. Caulfield of up to $1.2 million in connection with her joining the Company. Proceeds from the extension of credit may be drawn by Ms. Caulfield in one lump-sum or in periodic draws. As of April 2003, Ms. Caulfield had not elected to receive any amounts under the extension of credit. Any amounts drawn from the extension of credit would be due on the earliest of four years from when the extension of credit is drawn upon or when Ms. Caulfield leaves the Company. Interest would accrue at the IRS imputed rate of interest and is payable by Ms. Caulfield after two years.

Loan Arrangement with Dr. Nicholls

Pursuant to an extension of credit made to Dr. Nicholls on June 21, 2002, the Company made a $1,000,000 secured loan to assist him in relocating his principal place of residence to the United States. The loan is due and payable on the earliest of January 7, 2008, the sale of the house or when Dr. Nicholls leaves the Company. Interest on the loan accrues at the rate equal to the IRS imputed rate per annum. On a discretionary basis, up to 100% of the annual interest may be forgiven each year based on achievement of annual performance.